ROSMAP_MOFA_public_release

Public release of code and analyses related to Multi-omics Factor Analysis (MOFA) using data from the Religious Orders Study (ROS) and Rush Memory and Aging Project (MAP) cohorts.

This repository accompanies the preprint:

Citation

Scheidemantel LP, de Paiva Lopes K, Gaiteri C, Menon V, De Jager PL, Schneider JA, Buchman AS, Wang Y, Tasaki S, Raittz RT, Bennett DA, Vialle RA.
Integration of aged brain multi-omics reveals cross-system mechanisms underlying Alzheimer’s disease heterogeneity.
bioRxiv (2025). doi: 10.1101/2025.09.23.678110

Overview

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Key findings include:

  • Identification of cross-omic, cross-system biological factors linked to AD phenotypes.
  • Discovery of immune-related factors with both detrimental and protective associations.
  • Unsupervised clustering of participants into 11 molecular subtypes, including three AD-associated clusters with distinct molecular and phenotypic signatures.
  • Insights into neuroinflammatory processes, energetic metabolism, and cytoskeletal dynamics as central mechanisms in AD.

Repository Structure

  • 1.MOFA_analysis/ – Core MOFA implementation and factor extraction.
  • 2.GSEA_analysis/ – Gene Set Enrichment Analysis of MOFA factors.
  • 3.Loadings_analysis/ – Examination of omics loadings contributing to factors.
  • 4.Phenotypes_analysis/ – Associations between MOFA factors and AD phenotypes.
  • 5.Clustering_analysis/ – Unsupervised clustering of participants into molecular subtypes.
  • 6.Manuscript_code/ – Misc. scripts used to generate other figures and results.

Distributed under terms of the GNU GENERAL PUBLIC LICENSE.